Understanding bread wheat’s genomic diversity and signature of selection characterized using genotyping-by-sequencing data

Description of the topic

The CIMMYT Global Wheat Program (GWP) develops large numbers of elite wheat lines that are distributed to national partners. The best lines are directly released or used as parents in the development of cultivars worldwide. As germplasm undergoes years of intense selection, some regions of the genome become fixed and show limited diversity, while other regions maintain diversity. The major objective of this study is to understand the genomic diversity of GWP germplasm characterized using high density genotyping-by-sequencing (GBS) data. More detailed objectives of this study are to: (1) study the genetic diversity of the breeding germplasm using all the genomic data (“global” diversity) versus genome-specific data (markers specific to the “A”, “B” or “D” genomes); (2) evaluate region-specific variation (“local” diversity in terms of haplotypes) in surrounding regions of the genome that contributed to the Green Revolution (disease resistance, plant height, photoperiod) or other important genes; and (3) understand the signatures of selection. CIMMYT’s wheat molecular breeding unit has already genotyped more than 20,000 individuals using GBS and single nucleotide polymorphism (SNP) markers. In addition, these individuals have comprehensive pedigree and phenotypic information. By looking at these patterns across the genome, it may be possible to predict candidates or parents for new cross combinations that could lead to high yielding cultivars. The comprehensive genomic profile could also help to increase allelic diversity in target genomic regions. Thus, this project will help ongoing conventional and hybrid breeding programs develop new strategies.

Work expectations

The candidate is expected to collaborate with the GWP and other relevant programs. CIMMYT already has a comprehensive collection of pedigree, phenotypic and marker data. The candidate’s major activities will be to analyze the data, write reports and publish manuscripts.

Required skills

  • A basic understanding of plant breeding and molecular markers.
  • The candidate should have basic skills in any of the programming languages, but R, Python or Perl are desirable. By working with the supervisor(s), the candidate will have the opportunity of advancing his/her programming skills.
  • Good English writing and speaking skills.